2014 Publications

Amrine, K. C. H., Swingley, W. D., & Ardell, D. H. (2014). TRNA Signatures Reveal a Polyphyletic Origin of SAR11 Strains among Alphaproteobacteria. PLoS Computational Biology, 10(2), e1003454. https://doi.org/10.1371/journal.pcbi.1003454
Ananthakrishnan, R., Chard, K., Foster, I., & Tuecke, S. (2015). Globus platform-as-a-service for collaborative science applications. Concurrency and Computation: Practice and Experience, 27(2), 290–305.
Aronson, M. F. J., La Sorte, F. A., Nilon, C. H., Katti, M., Goddard, M. A., Lepczyk, C. A., Warren, P. S., Williams, N. S. G., Cilliers, S., Clarkson, B., Dobbs, C., Dolan, R., Hedblom, M., Klotz, S., Kooijmans, J. L., Kühn, I., MacGregor-Fors, I., McDonnell, M., Mörtberg, U., … Winter, M. (2014). A global analysis of the impacts of urbanization on bird and plant diversity reveals key anthropogenic drivers. Proceedings of the Royal Society B: Biological Sciences, 281(1780), 20133330. https://doi.org/10.1098/rspb.2013.3330
Aronson, M. F., La Sorte, F. A., Nilon, C. H., Katti, M., Goddard, M. A., Lepczyk, C. A., Warren, P. S., Williams, N. S., Cilliers, S., Clarkson, B., & others. (2014). A global analysis of the impacts of urbanization on bird and plant diversity reveals key anthropogenic drivers. Proceedings of the Royal Society B: Biological Sciences, 281(1780), 20133330.
Belamkar, V., Weeks, N. T., Bharti, A. K., Farmer, A. D., Graham, M. A., & Cannon, S. B. (2014). Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress. BMC Genomics, 15(1), 950. https://doi.org/10.1186/1471-2164-15-950
Brauer, E. K., Singh, D. K., & Popescu, S. C. (2014). Next-generation plant science: Putting big data to work. Genome Biology, 15(1), 301. https://doi.org/10.1186/gb4149
Brunbjerg, A. K., Cavender-Bares, J., Eiserhardt, W. L., Ejrnaes, R., Aarssen, L. W., Buckley, H. L., Forey, E., Jansen, F., Kattge, J., Lane, C., Lubke, R. A., Moles, A. T., Monserrat, A. L., Peet, R. K., Roncal, J., Wootton, L., & Svenning, J.-C. (2014). Multi-scale phylogenetic structure in coastal dune plant communities across the globe. Journal of Plant Ecology, 7(2), 101–114. https://doi.org/10.1093/jpe/rtt069
Buckner, Brent. (2014, January 11). Introducing Genome Browsers, Genome Structure, and Gene Annotation. Proceedings from Plant and Animal Gemone XXII.
Caciula, A. (2014). Optimization techniques for next-generation sequencing data analysis.
Campbell, M. S., Holt, C., Moore, B., & Yandell, M. (2014). Genome Annotation and Curation Using MAKER and MAKER-P: Genome Annotation and Curation Using MAKER and MAKER-P. In A. Bateman, W. R. Pearson, L. D. Stein, G. D. Stormo, & J. R. Yates (Eds.), Current Protocols in Bioinformatics (p. 4.11.1-4.11.39). John Wiley & Sons, Inc. https://doi.org/10.1002/0471250953.bi0411s48
Cannon, S. B., McKain, M. R., Harkess, A., Nelson, M. N., Dash, S., Deyholos, M. K., Peng, Y., Joyce, B., Stewart, C. N., Rolf, M., Kutchan, T., Tan, X., Chen, C., Zhang, Y., Carpenter, E., Wong, G. K.-S., Doyle, J. J., & Leebens-Mack, J. (2015). Multiple Polyploidy Events in the Early Radiation of Nodulating and Nonnodulating Legumes. Molecular Biology and Evolution, 32(1), 193–210. https://doi.org/10.1093/molbev/msu296
Carnaby, P., Charters, S., Staincliffe, P., Cahalane, R., Laurenson, M., Gibb, R., McGlinchy, A., & Sutherland, S. (2014). Lincoln Hub data and information architecture project: DATA$^2$: Data architecture transforming access & analysis.
Chalhoub, B., Denoeud, F., Liu, S., Parkin, I. A. P., Tang, H., Wang, X., Chiquet, J., Belcram, H., Tong, C., Samans, B., Correa, M., Da Silva, C., Just, J., Falentin, C., Koh, C. S., Le Clainche, I., Bernard, M., Bento, P., Noel, B., … Wincker, P. (2014). Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 345(6199), 950–953. https://doi.org/10.1126/science.1253435
Chen, M., Mao, S., & Liu, Y. (2014). Big data: A survey. Mobile Networks and Applications, 19(2), 171–209.
Chen, M., Mao, S., Zhang, Y., & Leung, V. C. M. (2014). Big Data. Springer International Publishing. https://doi.org/10.1007/978-3-319-06245-7
Cholia, S., & Sun, T. (2014). The NEWT Platform: An Extensible Plugin Framework for Creating ReSTful HPC APIs. 2014 9th Gateway Computing Environments Workshop, 17–20. https://doi.org/10.1109/GCE.2014.14
Council, N. R., & others. (2012). Implementing the Research Strategy and Evaluating Progress. In A Research Strategy for Environmental, Health, and Safety Aspects of Engineered Nanomaterials. National Academies Press (US).
Crivelli, S., Dooley, R., Holmes, R., Mock, S., & The WeFold Community. (2015). Creating a gateway that enables large-scale science coopetition: LARGE-SCALE SCIENCE COOPETITION. Concurrency and Computation: Practice and Experience, 27(2), 446–457. https://doi.org/10.1002/cpe.3270
Cuccuru, G., Leo, S., Lianas, L., Muggiri, M., Pinna, A., Pireddu, L., Uva, P., Angius, A., Fotia, G., & Zanetti, G. (2014). An automated infrastructure to support high-throughput bioinformatics. 2014 International Conference on High Performance Computing & Simulation (HPCS), 600–607. https://doi.org/10.1109/HPCSim.2014.6903742
Dahdul, W. M., Cui, H., Mabee, P. M., Mungall, C. J., Osumi-Sutherland, D., Walls, R. L., & Haendel, M. A. (2014). Nose to tail, roots to shoots: Spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. Journal of Biomedical Semantics, 5(1), 34. https://doi.org/10.1186/2041-1480-5-34
Das, A., Bucksch, A., Price, C. A., & Weitz, J. S. (2014). ClearedLeavesDB: An online database of cleared plant leaf images. Plant Methods, 10(1), 8. https://doi.org/10.1186/1746-4811-10-8
Das, A., Bucksch, A., & Weitz, J. S. (n.d.). Infrastructure for managing and analyzing biological networks derived from collections of plant images.
Der, Joshua P. (2014, January 14). A unified global gene family classification resource for plants and its utility for comparative genomics, genome annotation, and gene family studies. Proceedings from Plant and Animal Gemone XXII.
Dooley, R., & Stubbs, J. (2014). Dynamically Provisioning Portable Gateway Infrastructure Using Docker and Agave. Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE ’14, 1–2. https://doi.org/10.1145/2616498.2616561
Duvick, Jon. (2014, January 14). Genome annotation in the cloud through xGDBvm virtual server instances deployed at iPlant. Proceedings from Plant and Animal Gemone XXII.
Esa. (2014). The 2014 Annual Reports to the Governing Council: ESA 99 th Annual Meeting, Sacramento, California, August 9 th -15 th , 2014. Bulletin of the Ecological Society of America, 95(4), S1–S69. https://doi.org/10.1890/2014.councilreport
Feltus, F. A. (2014). Systems genetics: A paradigm to improve discovery of candidate genes and mechanisms underlying complex traits. Plant Science, 223, 45–48. https://doi.org/10.1016/j.plantsci.2014.03.003
Gardiner, L.-J., Gawroński, P., Olohan, L., Schnurbusch, T., Hall, N., & Hall, A. (2014). Using genic sequence capture in combination with a syntenic pseudo genome to map a deletion mutant in a wheat species. The Plant Journal, 80(5), 895–904. https://doi.org/10.1111/tpj.12660
Gnimpieba, E. Z., Chango, A., & Lushbough, C. M. (2014). RNA-seq gene and transcript expression analysis using the BioExtract server and iPlant collaborative. Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB ’14, 661–669. https://doi.org/10.1145/2649387.2660822
Goodrich, J. K., Di Rienzi, S. C., Poole, A. C., Koren, O., Walters, W. A., Caporaso, J. G., Knight, R., & Ley, R. E. (2014). Conducting a Microbiome Study. Cell, 158(2), 250–262. https://doi.org/10.1016/j.cell.2014.06.037
Gorton, I. (2013). Cyberinfrastructures: Bridging the divide between scientific research and software engineering. Computer, 47(8), 48–55.
Han Hu, Yonggang Wen, Tat-Seng Chua, & Xuelong Li. (2014). Toward Scalable Systems for Big Data Analytics: A Technology Tutorial. IEEE Access, 2, 652–687. https://doi.org/10.1109/ACCESS.2014.2332453
Hanlon, M. R., Vaughn, M., Mock, S., Dooley, R., Moreira, W., Stubbs, J., Town, C., Miller, J., Krishnakumar, V., Ferlanti, E., & Pence, E. (2014). The Arabidopsis Information Portal: An Application Platform for Data Discovery. 2014 9th Gateway Computing Environments Workshop, 38–41. https://doi.org/10.1109/GCE.2014.10
Hart, D. L., Schuele, A., Soriano, E., Dahan, M., & Hanlon, M. (2014). XRAS: Allocations software as a service in XSEDE. Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE ’14, 1–8. https://doi.org/10.1145/2616498.2616562
Hilgert, U., McKay, S., Khalfan, M., Williams, J., Ghiban, C., & Micklos, D. (2014). DNA Subway: Making Genome Analysis Egalitarian. Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE ’14, 1–3. https://doi.org/10.1145/2616498.2616575
Holmgren, C. A., Betancourt, J. L., Peñalba, M. C., Delgadillo, J., Zuravnsky, K., Hunter, K. L., Rylander, K. A., & Weiss, J. L. (2014). Evidence against a Pleistocene desert refugium in the Lower Colorado River Basin. Journal of Biogeography, 41(9), 1769–1780. https://doi.org/10.1111/jbi.12337
Horvath, D., James V. Anderson, Munevver Dogramaci, & Brian Scheffler. (2014, January 14). Progress in Sequencing the Genome of an Invasive Polyploid Weed (Leafy Spurge). Proceedings from Plant and Animal Gemone XXII.
Huang, P., Feldman, M., Schroder, S., Bahri, B. A., Diao, X., Zhi, H., Estep, M., Baxter, I., Devos, K. M., & Kellogg, E. A. (2014). Population genetics of Setaria viridis , a new model system. Molecular Ecology, 23(20), 4912–4925. https://doi.org/10.1111/mec.12907
Hurwitz, B. L., Westveld, A. H., Brum, J. R., & Sullivan, M. B. (2014). Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses. Proceedings of the National Academy of Sciences, 111(29), 10714–10719. https://doi.org/10.1073/pnas.1319778111
Hurwitz, Bonnie. (2014, January 14). iMicrobe: Advancing Clinical and Environmental Microbial Research using the iPlant Cyberinfrastructure. Proceedings from Plant and Animal Gemone XXII.
Hurwitz, Bonnie L, Brum, J. R., & Sullivan, M. B. (2015). Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome. The ISME Journal, 9(2), 472–484. https://doi.org/10.1038/ismej.2014.143
Ichihashi, Y., Aguilar-Martinez, J. A., Farhi, M., Chitwood, D. H., Kumar, R., Millon, L. V., Peng, J., Maloof, J. N., & Sinha, N. R. (2014). Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape. Proceedings of the National Academy of Sciences, 111(25), E2616–E2621. https://doi.org/10.1073/pnas.1402835111
Izquierdo-Carrasco, F., Cazes, J., Smith, S. A., & Stamatakis, A. (2014). PUmPER: phylogenies updated perpetually. Bioinformatics, 30(10), 1476–1477.
Jamann, T. M., Poland, J. A., Kolkman, J. M., Smith, L. G., & Nelson, R. J. (2014). Unraveling Genomic Complexity at a Quantitative Disease Resistance Locus in Maize. Genetics, 198(1), 333–344. https://doi.org/10.1534/genetics.114.167486
Kanewala, T. A., Marru, S., Basney, J., & Pierce, M. (2014). A Credential Store for Multi-tenant Science Gateways. 2014 14th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, 445–454. https://doi.org/10.1109/CCGrid.2014.95
Katz, D. S., Choi, S.-C. T., Lapp, H., Maheshwari, K., Löffler, F., Turk, M., Hanwell, M. D., Wilkins-Diehr, N., Hetherington, J., Howison, J., Swenson, S., Allen, G. D., Elster, A. C., Berriman, B., & Venters, C. (2014). Summary of the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1). Journal of Open Research Software, 2(1), e6. https://doi.org/10.5334/jors.an
Kim, G., LeBlanc, M. L., Wafula, E. K., dePamphilis, C. W., & Westwood, J. H. (2014). Genomic-scale exchange of mRNA between a parasitic plant and its hosts. Science, 345(6198), 808–811. https://doi.org/10.1126/science.1253122
Koesterke, L., Koltes, J. E., Weeks, N. T., Milfeld, K., Vaughn, M. W., Reecy, J. M., & Stanzione, D. (2014). Discovery of biological networks using an optimized partial correlation coefficient with information theory algorithm on Stampede’s Xeon and Xeon Phi processors: ACCELERATED BIOLOGICAL NETWORK DISCOVERY WITH PCIT. Concurrency and Computation: Practice and Experience, 26(13), 2178–2190. https://doi.org/10.1002/cpe.3252
Krishnakumar, V., Hanlon, M. R., Contrino, S., Ferlanti, E. S., Karamycheva, S., Kim, M., Rosen, B. D., Cheng, C.-Y., Moreira, W., Mock, S. A., Stubbs, J., Sullivan, J. M., Krampis, K., Miller, J. R., Micklem, G., Vaughn, M., & Town, C. D. (2015). Araport: The Arabidopsis Information Portal. Nucleic Acids Research, 43(D1), D1003–D1009. https://doi.org/10.1093/nar/gku1200
Lammers, Y., Peelen, T., Vos, R. A., & Gravendeel, B. (2014). The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data. BMC Bioinformatics, 15(1), 44. https://doi.org/10.1186/1471-2105-15-44
Law, M., Childs, K. L., Campbell, M. S., Stein, J. C., Olson, A. J., Holt, C., Panchy, N., Lei, J., Jiao, D., Andorf, C. M., Lawrence, C. J., Ware, D., Shiu, S.-H., Sun, Y., Jiang, N., & Yandell, M. (2015). Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes. Plant Physiology, 167(1), 25–39. https://doi.org/10.1104/pp.114.245027
Lawrence, K. A., Wilkins-Diehr, N., Wernert, J. A., Pierce, M., Zentner, M., & Marru, S. (2014). Who Cares about Science Gateways? A Large-Scale Survey of Community Use and Needs. 2014 9th Gateway Computing Environments Workshop, 1–4. https://doi.org/10.1109/GCE.2014.11
Liu, Yang et al. (2015, January 12). Large-Scale Next-Generation Resequencing of Soybean Germplasm for Trait Discovery. Proceedings from Plant and Animal Genome XXIII.
Lushbough, C. M., Gnimpieba, E. Z., & Dooley, R. (2015). Life science data analysis workflow development using the bioextract server leveraging the iPlant collaborative cyberinfrastructure: BIOEXTRACT SERVER WORKFLOWS LEVERAGING IPLANT COLLABORATIVE. Concurrency and Computation: Practice and Experience, 27(2), 408–419. https://doi.org/10.1002/cpe.3237
Ma, C., Zhang, H. H., & Wang, X. (2014). Machine learning for Big Data analytics in plants. Trends in Plant Science, 19(12), 798–808. https://doi.org/10.1016/j.tplants.2014.08.004
Ma, L., & Hunt, A. G. (2015). A 3′ RACE Protocol to Confirm Polyadenylation Sites. In A. G. Hunt & Q. Q. Li (Eds.), Polyadenylation in Plants (Vol. 1255, pp. 135–144). Springer New York. https://doi.org/10.1007/978-1-4939-2175-1_12
Maia, V. H., Gitzendanner, M. A., Soltis, P. S., Wong, G. K.-S., & Soltis, D. E. (2014). Angiosperm phylogeny based on 18S/26S rDNA sequence data: Constructing a large data set using next-generation sequence data. International Journal of Plant Sciences, 175(6), 613–650.
Makinde, D. (2014). African Orphan Crops Consortium: A NEPAD-led initiative. Viewpoints: Africa’s Future... Can Biosciences Contribute, 57.
Mandadi, K. K., & Karen-Beth G. Scholthof. (2014, January 14). Transcriptomic Analyses and Alternative Splicing Landscapes of Brachypodium Infected with Panicum Mosaic Virus. Proceedings from Plant and Animal Gemone XXII.
Martin, L., Cook, C., Matasci, N., Williams, J., & Bastow, R. (2015). Data mining with iPlant: A meeting report from the 2013 GARNet workshop, Data mining with iPlant. Journal of Experimental Botany, 66(1), 1–6. https://doi.org/10.1093/jxb/eru402
Matasci, N., Hung, L.-H., Yan, Z., Carpenter, E. J., Wickett, N. J., Mirarab, S., Nguyen, N., Warnow, T., Ayyampalayam, S., Barker, M., Burleigh, J. G., Gitzendanner, M. A., Wafula, E., Der, J. P., dePamphilis, C. W., Roure, B., Philippe, H., Ruhfel, B. R., Miles, N. W., … Wong, G. K.-S. (2014). Data access for the 1,000 Plants (1KP) project. GigaScience, 3(1), 17. https://doi.org/10.1186/2047-217X-3-17
McDonald, J., & Hart, S. (2012). Latest Technology in Irrigation Management in Nursery Production\copyright. Proceedings of the International Plant Propagators Society-2012 1014, 89–93.
Melicher, D., Torson, A. S., Dworkin, I., & Bowsher, J. H. (2014). A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach. BMC Genomics, 15(1), 188. https://doi.org/10.1186/1471-2164-15-188
Mentewab, A., Matheson, K., Adebiyi, M., Robinson, S., & Elston, B. (2014). RNA-seq analysis of the effect of kanamycin and the ABC transporter AtWBC19 on Arabidopsis thaliana seedlings reveals changes in metal content. PloS One, 9(10), e109310.
Merelli, I., Pérez-Sánchez, H., Gesing, S., & D’Agostino, D. (2014a). High-Performance Computing and Big Data in Omics-Based Medicine. BioMed Research International, 2014, 1–2. https://doi.org/10.1155/2014/825649
Merelli, I., Pérez-Sánchez, H., Gesing, S., & D’Agostino, D. (2014b). Managing, analysing, and integrating big data in medical bioinformatics: Open problems and future perspectives. BioMed Research International, 2014.
Michaletz, S. T., Cheng, D., Kerkhoff, A. J., & Enquist, B. J. (2014). Convergence of terrestrial plant production across global climate gradients. Nature, 512(7512), 39–43. https://doi.org/10.1038/nature13470
Micklos, Dave. (2014, January 11). A Simple Bioinformatics Workflow for RNA-Seq Analysis and Distributed Genome Annotation. Proceedings from Plant and Animal Gemone XXII.
Mirarab, S., Reaz, R., Bayzid, Md. S., Zimmermann, T., Swenson, M. S., & Warnow, T. (2014). ASTRAL: Genome-scale coalescent-based species tree estimation. Bioinformatics, 30(17), i541–i548. https://doi.org/10.1093/bioinformatics/btu462
Mirarab, Siavash, Bayzid, M. S., Boussau, B., & Warnow, T. (2014a). Avian Model Species Trees for 1X Model Condition for Mirarab et. Al.
Mirarab, Siavash, Bayzid, M. S., Boussau, B., & Warnow, T. (2014b). Bin Definition for Super Gene Trees for Mirarab et. Al.
Mirarab, Siavash, Bayzid, M. S., Boussau, B., & Warnow, T. (2014c). Binning Code for Mirarab et. Al.
Mirarab, Siavash, Bayzid, M. S., Boussau, B., & Warnow, T. (2014d). Sequence Alignments and Trees for Avian 1X for Mirarab et. Al.
Mirarab, Siavash, Nguyen, N., Guo, S., Wang, L.-S., Kim, J., & Warnow, T. (2015). PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. Journal of Computational Biology, 22(5), 377–386. https://doi.org/10.1089/cmb.2014.0156
Mirarab, Siavash, Nguyen, N., & Warnow, T. (2014). PASTA: ultra-large multiple sequence alignment. International Conference on Research in Computational Molecular Biology, 177–191.
Mohan, A., Hacker, T., Rodgers, G. P., & Islam, T. (2014). Batchsubmit: A high-volume batch submission system for earthquake engineering simulation: BATCHSUBMIT: A HIGH-VOLUME BATCH SUBMISSION SYSTEM. Concurrency and Computation: Practice and Experience, 26(13), 2240–2252. https://doi.org/10.1002/cpe.3234
Nezhad, A. S. (2014). Future of portable devices for plant pathogen diagnosis. Lab Chip, 14(16), 2887–2904. https://doi.org/10.1039/C4LC00487F
Ningthoujam, S. S., Choudhury, M. D., Potsangbam, K. S., Chetia, P., Nahar, L., Sarker, S. D., Basar, N., & Talukdar, A. D. (2014). NoSQL Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources: NoSQL Data Model for Integration of Ethnomedicinal Plant Data. Phytochemical Analysis, 25(6), 495–507. https://doi.org/10.1002/pca.2520
Oaks, J. R. (2014). An Improved Approximate-Bayesian Model-choice Method for Estimating Shared Evolutionary History. BMC Evolutionary Biology, 14(1), 150. https://doi.org/10.1186/1471-2148-14-150
Oaks, J. R., Linkem, C. W., & Sukumaran, J. (2014). Implications of uniformly distributed, empirically informed priors for phylogeographical model selection: A reply to Hickerson et al. Evolution, 68(12), 3607–3617. https://doi.org/10.1111/evo.12523
Parr, C. S., Wilson, N., Leary, P., Schulz, K., Lans, K., Walley, L., Hammock, J., Goddard, A., Rice, J., Studer, M., Holmes, J., & Corrigan, Jr., R. (2014). The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth. Biodiversity Data Journal, 2, e1079. https://doi.org/10.3897/BDJ.2.e1079
Parry, G. (2014). Components of the Arabidopsis nuclear pore complex play multiple diverse roles in control of plant growth. Journal of Experimental Botany, 65(20), 6057–6067. https://doi.org/10.1093/jxb/eru346
Poelchau, M., Childers, C., Moore, G., Tsavatapalli, V., Evans, J., Lee, C.-Y., Lin, H., Lin, J.-W., & Hackett, K. (2015). The i5k Workspace@NAL—enabling genomic data access, visualization and curation of arthropod genomes. Nucleic Acids Research, 43(D1), D714–D719. https://doi.org/10.1093/nar/gku983
Poelchau, M. F., Huang, X., Goff, A., Reynolds, J., & Armbruster, P. (2014). An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus. Journal of Visualized Experiments, 93, 51961. https://doi.org/10.3791/51961
Poldrack, R. A., & Poline, J.-B. (2015). The publication and reproducibility challenges of shared data. Trends in Cognitive Sciences, 19(2), 59–61. https://doi.org/10.1016/j.tics.2014.11.008
Rajasekar, A., Xu, H., & Moore, R. (2014). Note on Three Classes of Data Grid Operations. Journal of Computer and Communications, 02(06), 1–6. https://doi.org/10.4236/jcc.2014.26001
Rajasekar, Arcot. (n.d.). The Librarian & the Big Data: Bridging the Gap. Proceedings from the 2014 E-Science Symposium at University of Massachusetts Medical School.
Ranjan, A., Ichihashi, Y., Farhi, M., Zumstein, K., Townsley, B., David-Schwartz, R., & Sinha, N. R. (2014). De Novo Assembly and Characterization of the Transcriptome of the Parasitic Weed Dodder Identifies Genes Associated with Plant Parasitism. PLANT PHYSIOLOGY, 166(3), 1186–1199. https://doi.org/10.1104/pp.113.234864
Reecy, J., J.P. Carson, F. McCarthy, J.E. Koltes, E. Friz-Waters, J. Williams, E. Lyons, C.F. Baes, & M.W. Vaughn. (2014). Cyberinfrastructure for Life Sciences—IAnimal resources for genomics and other data driven biology. Proceedings, 10th World Congress of Genetics Applied to Livestock Production, 9911.
Reecy, James, C. Baes, E. Fritz-Waters, James E. Koltes, M. Dolezal, B. Bapts, C. Flury, H. Signer-Hasler, C. Stricker, Rohan L. Fernando, Dorian J. Garrick., Fritz Schmitz-Hsu, B. Gredler, & Matt Vaughn. (2014). Computational resources to facilitate variant discovery and analysis. In ADSA-ASAS Midwest Meeting, 23.
Rees, T. (2014). Taxamatch, an Algorithm for Near (‘Fuzzy’) Matching of Scientific Names in Taxonomic Databases. PLoS ONE, 9(9), e107510. https://doi.org/10.1371/journal.pone.0107510
Robinson, N., Regetz, J., & Guralnick, R. P. (2014). EarthEnv-DEM90: A nearly-global, void-free, multi-scale smoothed, 90m digital elevation model from fused ASTER and SRTM data. ISPRS Journal of Photogrammetry and Remote Sensing, 87, 57–67. https://doi.org/10.1016/j.isprsjprs.2013.11.002
Ruhfel, B. R., Gitzendanner, M. A., Soltis, P. S., Soltis, D. E., & Burleigh, J. (2014). From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evolutionary Biology, 14(1), 23. https://doi.org/10.1186/1471-2148-14-23
Sachdeva, P. S., Edmeades, G. O., Mumm, R. H., Rafalski, A. J., & Bennett, B. (2014). Report of the final external review of the Generation Challenge Programme.
Schatz, M. C., Maron, L. G., Stein, J. C., Hernandez Wences, A., Gurtowski, J., Biggers, E., Lee, H., Kramer, M., Antonio, E., Ghiban, E., Wright, M. H., Chia, J., Ware, D., McCouch, S. R., & McCombie, W. R. (2014). New whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica [Preprint]. Genomics. https://doi.org/10.1101/003764
Scott, T. (2014). Identification of GCN4 homologues in maize using a bioinformatics approach [PhD Thesis].
Shaffer, C. D., Alvarez, C. J., Bednarski, A. E., Dunbar, D., Goodman, A. L., Reinke, C., Rosenwald, A. G., Wolyniak, M. J., Bailey, C., Barnard, D., Bazinet, C., Beach, D. L., Bedard, J. E. J., Bhalla, S., Braverman, J., Burg, M., Chandrasekaran, V., Chung, H.-M., Clase, K., … Elgin, S. C. R. (2014). A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time. CBE—Life Sciences Education, 13(1), 111–130. https://doi.org/10.1187/cbe-13-08-0152
Šímová, I., Violle, C., Kraft, N. J. B., Storch, D., Svenning, J.-C., Boyle, B., Donoghue, J. C., Jørgensen, P., McGill, B. J., Morueta-Holme, N., Piel, W. H., Peet, R. K., Regetz, J., Schildhauer, M., Spencer, N., Thiers, B., Wiser, S., & Enquist, B. J. (2015). Shifts in trait means and variances in North American tree assemblages: Species richness patterns are loosely related to the functional space. Ecography, 38(7), 649–658. https://doi.org/10.1111/ecog.00867
Smith, H. C., Niewohner, D. J., Dewey, G. D., Longo, A. M., Guy, T. L., Higgins, B. R., Daehling, S. B., Genrich, S. C., Wentworth, C. D., & Durham Brooks, T. L. (2014). Using Flatbed Scanners to Collect High-resolution Time-lapsed Images of the Arabidopsis Root Gravitropic Response. Journal of Visualized Experiments, 83, 50878. https://doi.org/10.3791/50878
Snoderly-Foster, L. (2014). Characterization of a plant gene family expanded in glycine max.
Soderlund, C. A., Nelson, W. M., & Goff, S. A. (2014). Allele Workbench: Transcriptome Pipeline and Interactive Graphics for Allele-Specific Expression. PLoS ONE, 9(12), e115740. https://doi.org/10.1371/journal.pone.0115740
Stewart, C. A. (2014). Serving national scientific communities: Genome analysis as an example.
Stobbe, A. H., Schneider, W. L., Hoyt, P. R., & Melcher, U. (2014). Screening Metagenomic Data for Viruses Using the E-Probe Diagnostic Nucleic Acid Assay. Phytopathology, 104(10), 1125–1129. https://doi.org/10.1094/PHYTO-11-13-0310-R
Sullivan, M. B. (2015). Viromes, Not Gene Markers, for Studying Double-Stranded DNA Virus Communities. Journal of Virology, 89(5), 2459–2461. https://doi.org/10.1128/JVI.03289-14
Thavappiragasam, M., Lushbough, C. M., & Gnimpieba, E. Z. (2014a). Heuristic parallelizable algorithm for similarity based biosystems comparison. Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB ’14, 782–789. https://doi.org/10.1145/2649387.2660849
Thavappiragasam, M., Lushbough, C. M., & Gnimpieba, E. Z. (2014b). SBMLChecker, a Semantic approach for SBML model reliability evaluation. Proceedings of the International Conference on Bioinformatics & Computational Biology (BIOCOMP), 1.
The PLOS ONE Staff. (2014). Correction: De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum. PLoS ONE, 9(8), e105275. https://doi.org/10.1371/journal.pone.0105275
Tong, Q., Yuan, B., & Li, X. (2014). Cyberinfrastructure: Applications and challenges. 2014 International Conference on Smart Computing, 74–80.
Tukamuhabwa, L. A. (2014). Application of Bioinformatics in Crop Improvement: Annotating the Putative Soybean Rust resistance gene Rpp3 for Enhancing Marker Assisted Selection. Journal of Proteomics & Bioinformatics, 07(01). https://doi.org/10.4172/jpb.1000296
Uribe-Convers, S., Duke, J. R., Moore, M. J., & Tank, D. C. (2014). A Long PCR–Based Approach for DNA Enrichment Prior to Next-Generation Sequencing for Systematic Studies. Applications in Plant Sciences, 2(1), 1300063. https://doi.org/10.3732/apps.1300063
Vasquez-Gross, H., Jacob Zieve, Damian Gessler, David Neale, & Jill Wegrzyn. (2014, January 14). Case Study: Enabling Forest Tree Genomics through Association Studies with the use of SSWAP. Proceedings from Plant and Animal Gemone XXII.
Vaughn, Matt. (2014, January 13). The Arabidopsis Information Portal: A First Glimpse. Proceedings from Plant and Animal Gemone XXII.
Verborgh, R., Harth, A., Maleshkova, M., Stadtmüller, S., Steiner, T., Taheriyan, M., & Van de Walle, R. (2014). Survey of Semantic Description of REST APIs. In C. Pautasso, E. Wilde, & R. Alarcon (Eds.), REST: Advanced Research Topics and Practical Applications (pp. 69–89). Springer New York. https://doi.org/10.1007/978-1-4614-9299-3_5
Walls, R., John Deck, Robert Guralnick, & Andrea Matsunaga. (n.d.). A Specimen-based View of the World: Using the Biological Collections Ontology to Model Biodiversity Collections. CEUR Workshop Proceedings. http://ceur-ws.org/Vol-1309/paper8.pdf
Walls, R. L., Deck, J., Guralnick, R., Baskauf, S., Beaman, R., Blum, S., Bowers, S., Buttigieg, P. L., Davies, N., Endresen, D., Gandolfo, M. A., Hanner, R., Janning, A., Krishtalka, L., Matsunaga, A., Midford, P., Morrison, N., Tuama, É. Ó., Schildhauer, M., … Wooley, J. (2014). Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies. PLoS ONE, 9(3), e89606. https://doi.org/10.1371/journal.pone.0089606
Walls, R. L., Guralnick, R., Deck, J., Buntzman, A., Buttigieg, P. L., Davies, N., Denslow, M. W., Gallery, R. E., Parnell, J. J., Osumi-Sutherland, D., Robbins, R. J., Rocca-Serra, P., Wieczorek, J., & Zheng, J. (2014). Meeting report: Advancing practical applications of biodiversity ontologies. Standards in Genomic Sciences, 9(1), 17. https://doi.org/10.1186/1944-3277-9-17
Wang, F., Niedermayr, C. V., & Liu, P. (2014). Metadata based management and sharing of distributed biomedical data. International Journal of Metadata, Semantics and Ontologies, 9(1), 42. https://doi.org/10.1504/IJMSO.2014.059126
Wang, L., Stein, L., & Ware, D. (2014). The relationships among GC content, nucleosome occupancy, and exon size. ArXiv:1404.2487 [q-Bio]. http://arxiv.org/abs/1404.2487
Wang, L., Ware, D., Lushbough, C., Merchant, N., & Stein, L. (2014). A GWAS platform built on iPlant cyber-infrastructure [Preprint]. Bioinformatics. https://doi.org/10.1101/002881
Wang, L., Ware, D., Lushbough, C., Merchant, N., & Stein, L. (2015). A genome-wide association study platform built on iPlant cyber-infrastructure: A GWAS PLATFORM BUILT ON iPLANT CYBER-INFRASTRUCTURE. Concurrency and Computation: Practice and Experience, 27(2), 420–432. https://doi.org/10.1002/cpe.3236
Weinandt, N., Jackson, L. M., Gnimpieba, E. Z., & Lushbough, C. (2014). Pheno2GRN: A workflow for phenotype to gene network study and reverse engineering comparison. Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB ’14, 797–804. https://doi.org/10.1145/2649387.2660851
Werner, G. D. A., Cornwell, W. K., Sprent, J. I., Kattge, J., & Kiers, E. T. (2014). A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms. Nature Communications, 5(1), 4087. https://doi.org/10.1038/ncomms5087
West, P. T., Li, Q., Ji, L., Eichten, S. R., Song, J., Vaughn, M. W., Schmitz, R. J., & Springer, N. M. (2014). Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome. PLoS ONE, 9(8), e105267. https://doi.org/10.1371/journal.pone.0105267
Wickett, N. J., Mirarab, S., Nguyen, N., Warnow, T., Carpenter, E., Matasci, N., Ayyampalayam, S., Barker, M. S., Burleigh, J. G., Gitzendanner, M. A., Ruhfel, B. R., Wafula, E., Der, J. P., Graham, S. W., Mathews, S., Melkonian, M., Soltis, D. E., Soltis, P. S., Miles, N. W., … Leebens-Mack, J. (2014). Phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences, 111(45), E4859–E4868. https://doi.org/10.1073/pnas.1323926111
Williams, C. M., Henry, H. A. L., & Sinclair, B. J. (2015). Cold truths: How winter drives responses of terrestrial organisms to climate change: Organismal responses to winter climate change. Biological Reviews, 90(1), 214–235. https://doi.org/10.1111/brv.12105
Williams, J., McKay, S., Khalfan, M., Ghiban, C., Hilgert, U., Lauter, S., Jeong, E., & Micklos, D. (2014). DNA Subway–An educational bioinformatics platform for gene and genome analysis: DNA barcoding, and RNA-Seq. 10th World Congress on Genetics Applied to Livestock Production.
Wilson, A. M., Parmentier, B., & Jetz, W. (2014). Systematic land cover bias in Collection 5 MODIS cloud mask and derived products—A global overview. Remote Sensing of Environment, 141, 149–154. https://doi.org/10.1016/j.rse.2013.10.025
Wilson-Sánchez, D., Rubio-Díaz, S., Muñoz-Viana, R., Pérez-Pérez, J. M., Jover-Gil, S., Ponce, M. R., & Micol, J. L. (2014). Leaf phenomics: A systematic reverse genetic screen for Arabidopsis leaf mutants. The Plant Journal, 79(5), 878–891. https://doi.org/10.1111/tpj.12595
Wofford, A. M., Finch, K., Bigott, A., & Willyard, A. (2014). A Set of Plastid Loci for Use in Multiplex Fragment Length Genotyping for Intraspecific Variation in Pinus (Pinaceae). Applications in Plant Sciences, 2(5), 1400002. https://doi.org/10.3732/apps.1400002
Xu, Dong. (2014, January 14). Soybean knowledge base (SoyKB): A web resource for integration of soybean translational genomics and molecular breeding. Proceedings from Plant and Animal Gemone XXII.
Xu, H., Ward, J. H., Conway, M., Rajasekar, A., & Moore, R. (2014). Building an extensible file system via policy-based data management. Proceedings of the 1st ACM International Workshop on Programmable File Systems - PFSW ’14, 11–18. https://doi.org/10.1145/2603941.2603943
Zhao, K., & Bartley, L. E. (2014). Comparative genomic analysis of the R2R3 MYB secondary cell wall regulators of Arabidopsis, poplar, rice, maize, and switchgrass. BMC Plant Biology, 14(1), 135. https://doi.org/10.1186/1471-2229-14-135